The American Society for Microbiology (ASM), the largest single life science Society with 39,000 members, wishes to submit the following recommendations in support of increased funding for the Fiscal Year 2015 budget for the Department of Energy (DOE) Office of Science. The DOE Office of Science has generated some of the Nation’s most economically important innovations and supports a large share of basic research in the physical sciences as well as critical areas of microbiological research. The DOE Office of Science supports research through six core programs: Advanced Scientific Computing Research, Basic Energy Sciences, Biological and Environmental Research, Fusion Energy Sciences, High Energy Physics and Nuclear Physics. Some of the most powerful scientific advances have emerged from intersections between these programs, such as the Human Genome Project integrating biology with computing to launch a biotechnology revolution, or new biofuel energy produced with microbial enzymes or improved microbial hosts.

The ASM strongly recommends increased funding for the DOE Office of Science and Biological and Environmental Research. In February, the National Science Board released its latest biennial measures of the US position in global R&D, confirming that US predominance in science and technology continues to falter as other nations accelerate their R&D investments. Since 2001, the US share of worldwide R&D decreased from 37 percent to 30 percent. Despite these unfortunate trends downward, the US is still investing twice as much in R&D as any other nation (though it has fallen to tenth place in terms of percentage of GDP). The US also has maintained its global lead in research publications, patents and monetary value of its R&D based intellectual property exports. It is vitally important that Congress continues to make increased investments in basic research and the biological and environmental research funded by the DOE Office of Science. The opportunities to generate knowledge that will spurn innovation and support US economic growth in the energy sector are too great to let advances from past investments move overseas.

DOE Office of Science funding has proven to be the motivational force in a number of fields that might otherwise stagnate. DOE funds intramural projects at DOE national laboratories and grant recipients at universities and other institutions across the US. Reports on R&D in the US regularly state the importance of federally funded university research in creating new companies and R&D jobs.

DOE Office of Science funding has built and operates more than 30 national scientific user facilities, which provide DOE and non-DOE researchers with the most advanced scientific tools, including supercomputers, particle accelerators, light sources and neutron sources and specialized facilities for studying the nanoworld or the environment. In FY 2012, over 29,000 researchers from academia, industry and government labs utilized these unique facilities to perform research that might have been impossible elsewhere. The Office of Science also operates 10 of the 17 DOE national laboratories across the United States. This February, university scientists reported key surface structures on the viruses causing dengue fever and West Nile fever that help the pathogens replicate and spread infection. Their research utilized DOE’s micro X-ray beam facility at Argonne National Laboratory to characterize the structures. The US R&D enterprise benefits immeasurably from this unparalleled network of large scale research facilities, the collective expertise of DOE technical staff and training programs for scientists, engineers and mathematicians.

Last May, DOE announced its fourth annual Early Career Research awards to boost the Nation’s scientific workforce, allocating up to $15.3 million for research by 61 scientists at US universities and national laboratories. DOE training grants help to ensure future expertise in critical R&D fields, many of which utilize microorganisms. For example, the 2013 R&D 100 Awards, which recognize top technology products, included products based on microbiology research at DOE laboratories: a lab kit that coordinates synthesis of foreign membrane proteins with synthesis of bacterial membranes to create membrane bound vesicles for use in drug discovery and other experiments; and a battery alternative that genetically modifies virus DNA to boost voltage produced by a biofilm of the virus (M13 phage), sandwiched between electrodes connected to external devices.

Office of Biological and Environmental Research (BER)

The Biological and Environmental Research (BER) program has built a reputation as world class innovator in large scale genomics, biofuels, biogeochemical processes like terrestrial carbon storage and soil contaminant migration and climate change modeling. BER supports both basic research and scientific user facilities that redefine the crucial US sectors of biotechnology, sustainable energy and environmental quality, with projects distributed between two divisions: Climate and Environmental Sciences (CESD) and Biological Systems Science (BSSD).

The Biological Systems Science Division administers the Agency’s programs in genomics based systems biology and radiological sciences, as well as the DOE Joint Genome Institute (JGI) and three DOE Bioenergy Research Centers. Using cutting edge genomics and powerful computing capability, BSSD supported research mines the genomes of microbial ecosystems to identify enzymes needed to process plant biomass, redesigns microbes for next generation biofuel production, advances understanding of global carbon cycle processes, and examines the role of biology in the fate of environmental contaminants. It also develops predictive computational models within the growing field of systems biology, along with tools for manipulating complex biosystems for practical applications. The JGI is a major user facility for genome sequencing that is an invaluable resource for the life sciences community.

BER is preeminent in basic microbiology relevant to energy, climate and environment and in reengineering these microorganisms, ensuring a high value return on federal investments of robust DOE funding. Among BER’s impressive impact are exciting possibilities of cellulosic and hydrocarbon based biofuels made from nonfood feedstocks, and algae directly replacing gasoline and other fuels. BER funded scientists are identifying microbes that most efficiently break down plant fiber, while others are genetically modifying microbes to directly produce fuel. Some projects incorporate collaborations among multiple universities, national laboratories, private companies and nonprofit organizations. These efforts have great potential for slowing the release of carbon dioxide into the atmosphere and reducing atmospheric concentrations of carbon dioxide which would alleviate concerns about the impacts of global climate change.

Recent DOE-BER Microbiology Research Highlights:

Recoding a Bacterial Genome Allows Biosynthesis of Proteins with New Functions -Researchers have been able to expand the possibilities of engineered protein functions by adding novel amino acids to the repertoire that can be incorporated into proteins. This work has tremendous implications for engineering new organisms that can be used for producing proteins that perform functions needed in DOE relevant processes, e.g. biofuels production.

New Metabolic Pathway Discovered in Methane-Consuming Bacteria -Recent technological advances in natural gas extraction from the deep subsurface also have vastly increased the supply of methane for energy production and potentially as an alternate carbon source for synthesis of fuels and other value-added chemicals. These developments have focused increased attention on biological processes that involve methane production. Research on the role of methanotrophs in environmental carbon cycle processes presents new opportunities for metabolic engineering of these organisms as platforms for biological conversion of methane to advanced biofuels and other products.

Novel Bioengineering Technique for Genome-Scale Tuning of Gene Expression - Introduction of new genes encoding desired functional attributes has long been a central tool for metabolic engineering and synthetic biodesign of microorganisms. Researchers developed a novel technique to more accurately predict gene expression levels in engineered biosystems. This new technique has the potential to allow much more sophisticated forward design of genetic engineering strategies to improve production of biofuels and other bioproducts.

Higher Yields of Advanced Biofuels from Genetically Engineered Yeast -The development of renewable substitutes for fuels and chemicals supplied by petroleum is an important aspect of achieving energy security. Ethanol is not an ideal gasoline replacement due to its low-energy density, handling challenges, and limited compatibility with the current transportation fleet. Focus has shifted to the production of advanced biofuels, designed to be “drop-in” fuels, having the same properties as gasoline, diesel, or jet fuel.

New Understanding of Microbial Community Processes Improves Carbon Cycle Models -Developing improved models of microbial processes will generate more accurate projections of soil carbon feedbacks on climate change and reduce a source of uncertainty in current Earth system models (ESMs).

Plants, Fungi, and Microbes: Symbiosis in Carbon and Nitrogen Cycling -Arbuscular mycorrhizal (AM) fungi form intimate affiliations with the roots of many plant types. This classic example of symbiosis is commonly understood to involve AM fungi helping the plants take up soil nutrients. In exchange, the fungi receive some of the sugars generated by the plants from photosynthesis. These findings reveal another layer of complexity in this symbiotic system and yield another important puzzle piece towards understanding the complex routes by which carbon and nitrogen flow through ecosystems.

Marginal Lands: A Valuable Resource for Sustainable Bioenergy Production -Growing plants on marginal lands, or lands unsuitable for conventional agricultural crops, is a promising route towards attaining sufficient cellulosic biomass for the production of biofuels without compromising food crops. If properly managed, marginal lands could provide sufficient biomass to support a viable cellulosic biofuel production industry while benefiting conservation efforts and the environment.

Watching Plant Biomass Breakdown to Improve Biofuel Production - Sustainable and cost effective production of biofuels from plant biomass is hindered by the cost of pretreatment and low sugar yields after enzymatic hydrolysis of plant cell wall polysaccharides. Scientists at the US Department of Energy’s (DOE) BioEnergy Science Center (BESC) and DOE National Renewable Energy Laboratory (NREL) are using a combination of advanced microscopic imaging methods to examine both fungal and bacterial enzyme systems. With this new technology, they are able to localize the enzymatic sites of action without compromising the cell wall’s structural integrity.

Soil Microbes Can Reduce Emissions of Nitrous Oxide, a Potent Greenhouse Gas -The use of large amounts of nitrogen fertilizer in modern agriculture has resulted in massive releases of nitrous oxide rather than molecular nitrogen into the atmosphere. In a new study, researchers have used a comparative genomics approach to identify new gene sequences involved in conversion of ammonia to molecular nitrogen, thus avoiding N2O production completely, and demonstrated that this genetic pathway is present in several abundant groups of soil microbes not previously thought to be involved in nitrogen conversion.

The Climate and Environmental Sciences (CES) Division plays a similarly unique role in research on terrestrial ecosystems, atmosphere, water and nutrient cycling in soils, climate change and environmental effects of energy production and use. Non-DOE researchers regularly access its user facilities (ARM Climate Research Facility and Environmental Molecular Sciences Laboratory), which provide the latest tools to analyze phenomena like contaminant mineral microbial interactions or biomarkers for disease. Recently reported CES supported work includes the discovery that soil containing high levels of certain types of symbiotic fungi contains about 70 percent more carbon than soils with other fungal types, a striking difference that might be attributable to varying fungal competition for nitrogen. Other research suggests that long term climate warming increases the microbial carbon use efficiency associated with degradation of complex carbon compounds such as phenol, but not of simple carbon compounds like glucose. Another CES focus, understanding the role of soil microorganisms in the fate and transport of environmental contaminants, continues to identify details important to environmental quality, such as the impact of bacterial biomass in the soil on which state of uranium is present, or finding a two gene cluster required by methylating bacteria to produce the neurotoxin methyl mercury from inorganic mercury in the environment.

The DOE Office of Science funding is vitally important to US innovation and economic growth and its programs clearly contribute to US global competitiveness in science and technology. The ASM urges Congress to fund the DOE Office of Science at the highest level possible in FY 2015. The DOE Office of Science advances science that addresses the growing challenges of energy and environmental change.